Variant report

Variant	rs960925
Chromosome Location	chr4:125120257-125120258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10011930	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021517	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11098744	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11732263	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11735374	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1357525	0.80[EUR][1000 genomes]
rs1370999	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523494	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1523497	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1523498	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1583687	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1811417	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1829521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114041	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4109176	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566664	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534428	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534434	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6834028	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843899	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847474	0.81[AMR][1000 genomes]
rs6857137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725001	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7657011	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs7664885	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7671916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681352	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7697184	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697326	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868977	chr4:124841128-125550637	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv432624	chr4:125013395-125367740	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998024	chr4:125019384-125380876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv537241	chr4:125019384-125380876	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015049	chr4:125037090-125393067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs960925	NDUFAF2	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125115400-125124800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:125120000-125120800	Enhancers	NHEK	skin
3	chr4:125120000-125121400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:125120000-125121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:125120000-125121600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:125120200-125121400	Enhancers	HMEC	breast
7	chr4:125120200-125121800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:125120200-125122200	Enhancers	Hela-S3	cervix

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